CS101 Introduction to Bioinformatics Programming

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==Objective==
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==Objectives==
This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or amino acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl programming and database management will be covered.  (This course is a combination of [[CS101A Perl for Biologists, Level 1]] and [[CS101C MySQL for Biologists, Level 1]].)
This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or amino acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl programming and database management will be covered.  (This course is a combination of [[CS101A Perl for Biologists, Level 1]] and [[CS101C MySQL for Biologists, Level 1]].)
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No database experience is required, just a need to learn how to work with databases. No programming experience is required, just a need to learn how to program.
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==Instructor==
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* [[Shailender Nagpal]]
==Syllabus==
==Syllabus==
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The course is divided into 8 sessions, roughly 1-1.5 hours each, and 2 sessions are held every day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.
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The on-line version of the course is divided into 8 sessions, 2 sessions per day, roughly 1-1.5 hours each day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.
* Session 1: Fundamentals of databases and deciding what to store. How to install a database management system (MySQL).
* Session 1: Fundamentals of databases and deciding what to store. How to install a database management system (MySQL).
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* Session 8: Installation of Perl packages, and some examples of using the famous package BioPerl, for manipulating sequences, automating BLAST queries, etc. A project will be assigned.
* Session 8: Installation of Perl packages, and some examples of using the famous package BioPerl, for manipulating sequences, automating BLAST queries, etc. A project will be assigned.
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==Required skills==
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{{Course footer
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|hours=6
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No database experience is required, just a need to learn how to work with databases. No programming experience is required, just a need to learn how to program.
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==Scheduled courses==
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This course has been offered several times. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, please register using instructions below.
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Upcoming:
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* [http://edu.bioinformatics.org/TCC Course TCC (online), March 9-13, 2009, 15:30-17:30 GMT daily]
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Completed:
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* [http://edu.bioinformatics.org/GTG Course GTG (online), December 8-12, 2008, 15:30-17:30 GMT daily]
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* [http://edu.bioinformatics.org/GGA Course GGA (online), September 15-19, 2008, 15:30-17:30 GMT daily]
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==Registration==
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Registration is done in two steps. First, if you haven't already done so, [https://edu.bioinformatics.org/login/signup.php create an online account] to access the educational section of our website. Second, register for this course by making a payment using either the online registration form (click on the scheduled course above; ''use this form only for credit card payments via secured PayPal''), or by sending in the [http://edu.bioinformatics.org/download/registration_form.pdf Mail-in registration form] (~150 kB PDF, ''use this form if paying by US checks, credit card or corporate purchase order''). Please check the tuition rates and discounts below.
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Registration deadline: When full
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==Tuition & discounts==
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The fee for this course is $995 USD (commercial, government)
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Discounted rates are available, as follows:
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* Academic and non-profit research organizations, $664
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* Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), please inquire.
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* [[Membership|Professional members]] get an additional 20% discount.
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* Limited scholarships may also be available for those in low-income economies.
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==Logistics==
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Online courses are offered via an online meeting system.  Access information will be provided prior to the start of the course. Each lecture will last 90 to 120 minutes, depending on the topics covered. For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as Flash videos (resolution reduced by 30%) each day, within one day.  Students will also be able to communicate with the instructor and other students via the course forums.  Lecture attendance is therefore not required.
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Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the [http://www.adobe.com/products/flashplayer/ Adobe Flash plugin].  A microphone and webcam are not required for this course.  The necessary software, lecture notes and exercises will be provided.
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==Certification==
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This course is certified by the [[Bioinformatics Organization|Bioinformatics Organization, Inc.]], the largest international affiliation in the field, and it will count as '''10''' "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
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==Additional information==
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If you have any questions, please send a message to [http://edu.bioinformatics.org/message/discussion.php?id=100003 J.W. Bizzaro] (login required) or call +1 978 562 4800.
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==See also==
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* [[CS101A Perl for Biologists, Level 1]]
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* [[CS101C MySQL for Biologists, Level 1]]
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* [[Educational services|Educational services at Bioinformatics.Org]]
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Revision as of 04:38, 5 November 2011

Contents

Objectives

This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or amino acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl programming and database management will be covered. (This course is a combination of CS101A Perl for Biologists, Level 1 and CS101C MySQL for Biologists, Level 1.)

No database experience is required, just a need to learn how to work with databases. No programming experience is required, just a need to learn how to program.

Instructor

Syllabus

The on-line version of the course is divided into 8 sessions, 2 sessions per day, roughly 1-1.5 hours each day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.

Scheduled courses

If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

Registration

Registration for courses at Bioinformatics.Org takes two steps:

Step 1
If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
Step 2
Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

Please also check the course tuition rates and discounts.

Registration deadline: When full

Tuition & discounts

Live instruction held on-line
Live instruction held on-site
On-demand instruction held on-line

Additional discounts are available as follows:

Logistics

The necessary software, lecture notes and exercises will be provided.

Live instruction held on-line

On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, depending on the topics covered.

For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as AVI video files each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.

Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and Java. A microphone and webcam are not required but may be used.

Certification

This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.

Refund policy

For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.

Additional information

Please contact us for questions or additional information.

See also

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